update docs

scvelo/datasets.py

@@ -5,7 +5,8 @@
 
 
 def dentategyrus():
-    """Dentate gyrus is part of the hippocampus involved in learning, episodic memory formation and spatial coding.
+    """Dentate Gyrus dataset from Hochgerner et al. (2018)
+    Dentate gyrus is part of the hippocampus involved in learning, episodic memory formation and spatial coding.
     It is measured using 10X Genomics Chromium and described in Hochgerner et al. (2018).
     The data consists of 25,919 genes across 3,396 cells and provides several interesting characteristics.
     """

scvelo/plotting/velocity.py

@@ -5,8 +5,8 @@
 def velocity(adata, var_names=None, basis='umap', mode='deterministic', fits='all', layers='all', color=None,
              fontsize=8, color_map='RdBu_r', size=.2, alpha=.5, ax=None, **kwargs):
     """Phase and velocity plot for set of genes
-
-    The phase plot shows Plots spliced against unspliced expressions with steady-state fit along with expression and velocity in embedding
+    The phase plot shows pliced against unspliced expressions with steady-state fit.
+    Further the embedding is shown colored by velocity and expression.
 
     Arguments
     ---------

scvelo/plotting/velocity_embedding.py

@@ -8,7 +8,7 @@ def velocity_embedding(adata, basis='umap', vbasis='velocity', layer=None, densi
                        legend_loc='right margin', legend_fontsize=None, legend_fontweight=None,
                        color_map=None, palette=None, frameon=False, right_margin=None, left_margin=None,
                        size=None, title=None, show=None, save=None, ax=None, **kwargs):
-    """Scatter plot with single cell velocities along observations or variables axes.
+    """Scatter plot with velocities along `.obs` or `.var` axes.
     Color the plot using annotations of observations (`.obs`), variables (`.var`) or expression of genes (`.var_names`).
 
     Arguments

scvelo/plotting/velocity_embedding_grid.py

@@ -67,7 +67,7 @@ def velocity_embedding_grid(adata, basis='umap', vbasis='velocity', density=1, c
                             legend_loc='right margin', legend_fontsize=None, legend_fontweight=None,
                             color_map=None, palette=None, frameon=False, right_margin=None, left_margin=None,
                             size=None, title=None, show=None, save=None, ax=None, **kwargs):
-    """Scatter plot with single cell velocities on a grid along observations or variables axes.
+    """Scatter plot with grid velocities along `.obs` or `.var` axes.
     Color the plot using annotations of observations (`.obs`), variables (`.var`) or expression of genes (`.var_names`).
 
     Arguments

scvelo/tools/velocity_graph.py

@@ -65,7 +65,6 @@ def compute(self, ixs):
 
 def velocity_graph(adata, vkey='velocity', n_recurse_neighbors=2, n_neighbors=None, n_jobs=1, sqrt_transform=False, copy=False):
     """Computes a velocity graph based on cosine similarities
-
     The cosine similarities are computed between velocities and potential cell state transitions
 
     Arguments